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Thomas Ferrin

Research Profile

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L Chen; X Chen; J F Costello; Thomas E Ferrin; K Fujii; C Hong; Susan J Johns; J Simko; Doug Stryke; C Wen; L Xu; Sook Wah Yee; E U Almof; E C Chen; Kathleen M Giacomini
Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3.
Zheng Yang; Thomas D Goddard; Conrad C Huang; Keren Lasker; Elaine C Meng; Eric F Pettersen; Andrej Sali; Dina Schneidman-Duhovny; Ben Webb; Thomas E Ferrin
UCSF Chimera, MODELLER, and IMP: an integrated modeling system.
Keren Lasker; Javier A Velázquez-Muriel; Benjamin M Webb; Zheng Yang; Thomas E Ferrin; Andrej Sali
Macromolecular assembly structures by comparative modeling and electron microscopy.

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All Publications

2013: L Chen; X Chen; J F Costello; Thomas E Ferrin; K Fujii; C Hong; Susan J Johns; J Simko; Doug Stryke; C Wen; L Xu; Sook Wah Yee; E U Almof; E C Chen; Kathleen M Giacomini
Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3.
The pharmacogenomics journal 2013;13(2):110-20.
2012: Zheng Yang; Thomas D Goddard; Conrad C Huang; Keren Lasker; Elaine C Meng; Eric F Pettersen; Andrej Sali; Dina Schneidman-Duhovny; Ben Webb; Thomas E Ferrin
UCSF Chimera, MODELLER, and IMP: an integrated modeling system.
Journal of structural biology 2012;179(3):269-78.
2012: Keren Lasker; Javier A Velázquez-Muriel; Benjamin M Webb; Zheng Yang; Thomas E Ferrin; Andrej Sali
Macromolecular assembly structures by comparative modeling and electron microscopy.
Methods in molecular biology (Clifton, N.J.) 2012;857():331-50.
2011: J H Choi; R L Davis; Thomas E Ferrin; Richard A Castro; S E Hesselson; G H Jang; G Jenkins; Susan J Johns; P J Joski; Pui-Yan Kwok; C A McCarty; J A Mefford; K M Morrissey; A H Ramirez; D M Roden; A Sali; A Schlessinger; Doug Stryke; R A Wilke; J S Witte; Sook Wah Yee; Kathleen M Giacomini
A common 5'-UTR variant in MATE2-K is associated with poor response to metformin.
Clinical pharmacology and therapeutics 2011;90(5):674-84.
2011: M J Kim; P Skewes-Cox; H Fukushima; S Hesselson; Sook Wah Yee; L B Ramsey; L Nguyen; J L Eshragh; Richard A Castro; C C Wen; Doug Stryke; Susan J Johns; Thomas E Ferrin; Pui-Yan Kwok; Mary Relling; Kathleen M Giacomini; Deanna L Kroetz; Nadav Ahituv
Functional characterization of liver enhancers that regulate drug-associated transporters.
Clinical pharmacology and therapeutics 2011;89(4):571-8.
2011: Leonard Apeltsin; John H Morris; Patricia C Babbitt; Thomas E Ferrin
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.
Bioinformatics (Oxford, England) 2011;27(3):326-33.
2011: John H Morris; Aaron M Newman; Gang Su; Tobias Wittkop; Leonard Apeltsin; Gary D Bader; Jan Baumbach; Thomas E Ferrin
clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
BMC bioinformatics 2011;12():436.
2011: Ursula Pieper; Benjamin M Webb; David T Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C Meng; Eric F Pettersen; Conrad C Huang; Ruchira S Datta; Parthasrathy Sampathkumar; Mallur S Madhusudhan; Kimmen Sjölander; Thomas E Ferrin; Stephen K Burley; Andrej Sali
ModBase, a database of annotated comparative protein structure models, and associated resources.
Nucleic acids research 2011;39(Database issue):D465-74.
2010: Ligong Chen; Bradley Pawlikowski; Avner Schlessinger; Swati S More; Doug Stryke; Susan J Johns; Michael A Portman; Eugene Chen; Thomas E Ferrin; Andrej Sali; Kathleen M Giacomini
Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin.
Pharmacogenetics and genomics 2010;20(11):687-99.
2010: John H Morris; Elaine C Meng; Thomas E Ferrin
Computational tools for the interactive exploration of proteomic and structural data.
Molecular & cellular proteomics : MCP 2010;9(8):1703-15.
2010: Avner Schlessinger; Pär Matsson; James E Shima; Ursula Pieper; Sook Wah Yee; Libusha Kelly; Leonard Apeltsin; Robert M Stroud; Thomas E Ferrin; Kathleen M Giacomini; Andrej Sali
Comparison of human solute carriers.
Protein science : a publication of the Protein Society 2010;19(3):412-28.
2009: Ji Ha Choi; Sook Wah Yee; Mee J Kim; Loan Nguyen; Jeong Ho Lee; Ji-One Kang; Stephanie Hesselson; Richard A Castro; Doug Stryke; Susan J Johns; Pui-Yan Kwok; Thomas E Ferrin; Min Goo Lee; Brian L Black; Nadav Ahituv; Kathleen M Giacomini
Identification and characterization of novel polymorphisms in the basal promoter of the human transporter, MATE1.
Pharmacogenetics and genomics 2009;19(10):770-80.
2009: Ying Chen; Kristen Teranishi; Shuanglian Li; Sook Wah Yee; Stephanie Hesselson; Doug Stryke; Susan J Johns; Thomas E Ferrin; Pui Kwok; Kathleen M Giacomini
Genetic variants in multidrug and toxic compound extrusion-1, hMATE1, alter transport function.
The pharmacogenomics journal 2009;9(2):127-36.
2009: Harunobu Tahara; Sook Wah Yee; Thomas J Urban; Stephanie Hesselson; Richard A Castro; Michiko Kawamoto; Doug Stryke; Susan J Johns; Thomas E Ferrin; Pui-Yan Kwok; Kathleen M Giacomini
Functional genetic variation in the basal promoter of the organic cation/carnitine transporters OCTN1 (SLC22A4) and OCTN2 (SLC22A5).
The Journal of pharmacology and experimental therapeutics 2009;329(1):262-71.
2009: Sook Wah Yee; James E Shima; Stephanie Hesselson; Loan Nguyen; Sarah De Val; Rachel J Lafond; Michiko Kawamoto; Susan J Johns; Doug Stryke; Pui-Yan Kwok; Thomas E Ferrin; Brian L Black; David Gurwitz; Nadav Ahituv; Kathleen M Giacomini
Identification and characterization of proximal promoter polymorphisms in the human concentrative nucleoside transporter 2 (SLC28A2).
The Journal of pharmacology and experimental therapeutics 2009;328(3):699-707.
2009: Stephanie E Hesselson; Pär Matsson; James E Shima; Hisayo Fukushima; Sook Wah Yee; Yuya Kobayashi; Jason M Gow; Connie Ha; Benjamin Ma; Annie Poon; Susan J Johns; Doug Stryke; Richard A Castro; Harunobu Tahara; Ji Ha Choi; Ligong Chen; Nicolas Picard; Elin Sjödin; Maarke J E Roelofs; Thomas E Ferrin; Richard Myers; Deanna L Kroetz; Pui-Yan Kwok; Kathleen M Giacomini
Genetic variation in the proximal promoter of ABC and SLC superfamilies: liver and kidney specific expression and promoter activity predict variation.
PloS one 2009;4(9):e6942.
2009: Holly J Atkinson; John H Morris; Thomas E Ferrin; Patricia C Babbitt
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.
PloS one 2009;4(2):e4345.
2008: Nada Abla; Leslie W Chinn; Tsutomu Nakamura; Li Liu; Conrad C Huang; Susan J Johns; Michiko Kawamoto; Doug Stryke; Travis R Taylor; Thomas E Ferrin; Kathleen M Giacomini; Deanna L Kroetz
The human multidrug resistance protein 4 (MRP4, ABCC4): functional analysis of a highly polymorphic gene.
The Journal of pharmacology and experimental therapeutics 2008;325(3):859-68.
2007: Thomas D Goddard; Thomas E Ferrin
Visualization software for molecular assemblies.
Current opinion in structural biology 2007;17(5):587-95.
2007: Thomas J Urban; Chen Yang; Leah L Lagpacan; Chaline Brown; Richard A Castro; Travis R Taylor; Conrad C Huang; Doug Stryke; Susan J Johns; Michiko Kawamoto; Elaine J Carlson; Thomas E Ferrin; Esteban González Burchard; Kathleen M Giacomini
Functional effects of protein sequence polymorphisms in the organic cation/ergothioneine transporter OCTN1 (SLC22A4).
Pharmacogenetics and genomics 2007;17(9):773-82.
2007: John H Morris; Conrad C Huang; Patricia C Babbitt; Thomas E Ferrin
structureViz: linking Cytoscape and UCSF Chimera.
Bioinformatics (Oxford, England) 2007;23(17):2345-7.
2007: Alex S Nord; Karen Vranizan; Whittemore Tingley; Alexander C Zambon; Kristina Hanspers; Loren G Fong; Yan Hu; Peter Bacchetti; Thomas E Ferrin; Patricia C Babbitt; Scott W Doniger; William C Skarnes; Stephen G Young; Bruce R Conklin
Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells.
PloS one 2007;2(7):e617.
2007: Thomas D Goddard; Conrad C Huang; Thomas E Ferrin
Visualizing density maps with UCSF Chimera.
Journal of structural biology 2007;157(1):281-7.
2006: Thomas J Urban; Renata C Gallagher; Chaline Brown; Richard A Castro; Leah L Lagpacan; Claire M Brett; Travis R Taylor; Elaine J Carlson; Thomas E Ferrin; Esteban González Burchard; Seymour Packman; Kathleen M Giacomini
Functional genetic diversity in the high-affinity carnitine transporter OCTN2 (SLC22A5).
Molecular pharmacology 2006;70(5):1602-11.
2006: Ilaria Badagnani; Richard A Castro; Travis R Taylor; Claire M Brett; Conrad C Huang; Doug Stryke; Michiko Kawamoto; Susan J Johns; Thomas E Ferrin; Elaine J Carlson; Esteban González Burchard; Kathleen M Giacomini
Interaction of methotrexate with organic-anion transporting polypeptide 1A2 and its genetic variants.
The Journal of pharmacology and experimental therapeutics 2006;318(2):521-9.
2006: Yasuo Yoshikuni; Thomas E Ferrin; Jay D Keasling
Designed divergent evolution of enzyme function.
Nature 2006;440(7087):1078-82.
2006: Andrew R Erdman; Lara M Mangravite; Thomas J Urban; Leah L Lagpacan; Richard A Castro; Melanie de la Cruz; Wendy Chan; Conrad C Huang; Susan J Johns; Michiko Kawamoto; Doug Stryke; Travis R Taylor; Elaine J Carlson; Thomas E Ferrin; Claire M Brett; Esteban González Burchard; Kathleen M Giacomini
The human organic anion transporter 3 (OAT3; SLC22A8): genetic variation and functional genomics.
American journal of physiology. Renal physiology 2006;290(4):F905-12.
2006: Ilaria Badagnani; Marco Sorani; Robert H Edwards; Chaline Brown; Richard A Castro; Conrad C Huang; Doug Stryke; Michiko Kawamoto; Susan J Johns; Elaine J Carlson; Travis Taylor; Wendy Chan; Melanie de la Cruz; Thomas E Ferrin; Esteban González Burchard; Ira Herskowitz; Deanna L Kroetz; Kathleen M Giacomini
PharmGKB submission update: VI. PMT submissions of genetic variations in neurotransmitter transporters (SLC6, SLC17, and SLC18) to the PharmGKB network.
Pharmacological reviews 2006;58(1):5-6.
2006: Yan Shu; Thomas J Urban; Maya K Leabman; Tomoe Fujita; Andrew R Erdman; Leah L Lagpacan; Chaline Brown; Richard A Castro; Conrad C Huang; Doug Stryke; Michiko Kawamoto; Susan J Johns; Travis R Taylor; Wendy Chan; Melanie de la Cruz; Elaine J Carlson; Thomas E Ferrin; Claire M Brett; Esteban González Burchard; Ira Herskowitz; Deanna L Kroetz; Kathleen M Giacomini
PharmGKB submission update: V. PMT submissions of genetic variation in SLC22 family transporters.
Pharmacological reviews 2006;58(1):3-4.
2006: Tan D Nguyen; Jason M Gow; Leslie W Chinn; Libusha Kelly; Hotcherl Jeong; Conrad C Huang; Doug Stryke; Michiko Kawamoto; Susan J Johns; Elaine Carlson; Travis Taylor; Thomas E Ferrin; Andrej Sali; Kathleen M Giacomini; Deanna L Kroetz
PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network.
Pharmacological reviews 2006;58(1):1-2.
2006: Scott C-H Pegg; Shoshana D Brown; Sunil Ojha; Jennifer L Seffernick; Elaine C Meng; John H Morris; Patricia J Chang; Conrad C Huang; Thomas E Ferrin; Patricia C Babbitt
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.
Biochemistry 2006;45(8):2545-55.
2006: Courtney A Harper; Conrad C Huang; Doug Stryke; Michiko Kawamoto; Thomas E Ferrin; Patricia C Babbitt
Comparison of methods for genomic localization of gene trap sequences.
BMC genomics 2006;7():236.
2006: Elaine C Meng; Eric F Pettersen; Gregory S Couch; Conrad C Huang; Thomas E Ferrin
Tools for integrated sequence-structure analysis with UCSF Chimera.
BMC bioinformatics 2006;7():339.
2006: Gregory S Couch; Donna K Hendrix; Thomas E Ferrin
Nucleic acid visualization with UCSF Chimera.
Nucleic acids research 2006;34(4):e29.
2006: Yasuo Yoshikuni; Vincent J J Martin; Thomas E Ferrin; Jay D Keasling
Engineering cotton (+)-delta-cadinene synthase to an altered function: germacrene D-4-ol synthase.
Chemistry & biology 2006;13(1):91-8.
2006: Alex S Nord; Patricia J Chang; Bruce R Conklin; Antony V Cox; Courtney A Harper; Geoffrey G Hicks; Conrad C Huang; Susan J Johns; Michiko Kawamoto; Songyan Liu; Elaine C Meng; John H Morris; Janet Rossant; Patricia Ruiz; William C Skarnes; Philippe Soriano; William L Stanford; Doug Stryke; Harald von Melchner; Wolfgang Wurst; Ken-ichi Yamamura; Stephen G Young; Patricia C Babbitt; Thomas E Ferrin
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
Nucleic acids research 2006;34(Database issue):D642-8.
2006: Ryan P Owen; Leah L Lagpacan; Travis R Taylor; Melanie de la Cruz; Conrad C Huang; Michiko Kawamoto; Susan J Johns; Doug Stryke; Thomas E Ferrin; Kathleen M Giacomini
Functional characterization and haplotype analysis of polymorphisms in the human equilibrative nucleoside transporter, ENT2.
Drug metabolism and disposition: the biological fate of chemicals 2006;34(1):12-5.
2005: Tomoe Fujita; Chaline Brown; Elaine J Carlson; Travis Taylor; Melanie de la Cruz; Susan J Johns; Doug Stryke; Michiko Kawamoto; Kazumi Fujita; Richard Castro; Chung-Wen Chen; Emil T Lin; Claire M Brett; Esteban González Burchard; Thomas E Ferrin; Conrad C Huang; Maya K Leabman; Kathleen M Giacomini
Functional analysis of polymorphisms in the organic anion transporter, SLC22A6 (OAT1).
Pharmacogenetics and genomics 2005;15(4):201-9.
2005: Thomas D Goddard; Conrad C Huang; Thomas E Ferrin
Software extensions to UCSF chimera for interactive visualization of large molecular assemblies.
Structure (London, England : 1993) 2005;13(3):473-82.
2005: Ryan P Owen; Jennifer H Gray; Travis R Taylor; Elaine J Carlson; Conrad C Huang; Michiko Kawamoto; Susan J Johns; Doug Stryke; Thomas E Ferrin; Kathleen M Giacomini
Genetic analysis and functional characterization of polymorphisms in the human concentrative nucleoside transporter, CNT2.
Pharmacogenetics and genomics 2005;15(2):83-90.
2005: Scott C-H Pegg; Shoshana Brown; Sunil Ojha; Conrad C Huang; Thomas E Ferrin; Patricia C Babbitt
Representing structure-function relationships in mechanistically diverse enzyme superfamilies.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005;():358-69.
2005: Thomas E Ferrin; Conrad C Huang; Daniel M Greenblatt; Doug Stryke; Kathleen M Giacomini; John H Morris
Enhancing data sharing in collaborative research projects with DASH.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005;():260-71.
2005: Ilaria Badagnani; Wendy Chan; Richard A Castro; Claire M Brett; Conrad C Huang; Doug Stryke; Michiko Kawamoto; Susan J Johns; Thomas E Ferrin; Elaine J Carlson; Esteban González Burchard; Kathleen M Giacomini
Functional analysis of genetic variants in the human concentrative nucleoside transporter 3 (CNT3; SLC28A3).
The pharmacogenomics journal 2005;5(3):157-65.
2004: Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Gregory S Couch; Daniel M Greenblatt; Elaine C Meng; Thomas E Ferrin
UCSF Chimera--a visualization system for exploratory research and analysis.
Journal of computational chemistry 2004;25(13):1605-12.
2004: Yan Shu; Maya K Leabman; Bo Feng; Lara M Mangravite; Conrad C Huang; Doug Stryke; Michiko Kawamoto; Susan J Johns; Joseph DeYoung; Elaine Carlson; Thomas E Ferrin; Ira Herskowitz; Kathleen M Giacomini
PharmGKB update: III. Genetic variants of SLC22A1, solute carrier family 22 (organic cation transporter), member 1.
Pharmacological reviews 2004;56(2):161.
2004: Jennifer H Gray; Lara M Mangravite; Ryan P Owen; Thomas J Urban; Wendy Chan; Elaine J Carlson; Conrad C Huang; Michiko Kawamoto; Susan J Johns; Doug Stryke; Thomas E Ferrin; Kathleen M Giacomini
Functional and genetic diversity in the concentrative nucleoside transporter, CNT1, in human populations.
Molecular pharmacology 2004;65(3):512-9.
2004: Ursula Pieper; Narayanan Eswar; Hannes Braberg; Mallur S Madhusudhan; Fred P Davis; Ashley C Stuart; Nebojsa Mirkovic; Andrea Rossi; maricus MR; András Fiser; Ben Webb; Daniel Greenblatt; Conrad C Huang; Thomas E Ferrin; Andrej Sali
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Nucleic acids research 2004;32(Database issue):D217-22.
2003: Maya K Leabman; Conrad C Huang; Doug Stryke; Susan J Johns; Michiko Kawamoto; Thomas E Ferrin; Joseph DeYoung; Travis R Taylor; Melanie de la Cruz; Ira Herskowitz; Kathleen M Giacomini
PharmGKB update: I. Genetic variants of the organic cation transporter 2 (OCT2, SLC22A2).
Pharmacological reviews 2003;55(3):399.
2003: Deanna L Kroetz; Christiane Pauli-Magnus; Laura M Hodges; Conrad C Huang; Michiko Kawamoto; Susan J Johns; Doug Stryke; Thomas E Ferrin; Joseph DeYoung; Travis Taylor; Elaine J Carlson; Ira Herskowitz; Kathleen M Giacomini; andrew clark
Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene.
Pharmacogenetics 2003;13(8):481-94.
2003: Yan Shu; Maya K Leabman; Bo Feng; Lara M Mangravite; Conrad C Huang; Doug Stryke; Michiko Kawamoto; Susan J Johns; Joseph DeYoung; Elaine Carlson; Thomas E Ferrin; Ira Herskowitz; Kathleen M Giacomini
Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(10):5902-7.
2003: Maya K Leabman; Conrad C Huang; Joseph DeYoung; Elaine J Carlson; Travis R Taylor; Melanie de la Cruz; Susan J Johns; Doug Stryke; Michiko Kawamoto; Thomas J Urban; Deanna L Kroetz; Thomas E Ferrin; andrew clark; Neil Risch; Ira Herskowitz; Kathleen M Giacomini
Natural variation in human membrane transporter genes reveals evolutionary and functional constraints.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(10):5896-901.
2003: Douglas H Osato; Conrad C Huang; Michiko Kawamoto; Susan J Johns; Doug Stryke; Joanne Wang; Thomas E Ferrin; Ira Herskowitz; Kathleen M Giacomini
Functional characterization in yeast of genetic variants in the human equilibrative nucleoside transporter, ENT1.
Pharmacogenetics 2003;13(5):297-301.
2003: Andrew I Jewett; Conrad C Huang; Thomas E Ferrin
MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance.
Bioinformatics (Oxford, England) 2003;19(5):625-34.
2003: Doug Stryke; Conrad C Huang; Michiko Kawamoto; Susan J Johns; Elaine J Carlson; Joseph DeYoung; Maya K Leabman; Ira Herskowitz; Kathleen M Giacomini; Thomas E Ferrin
SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003;():535-47.
2003: Ranyee A Chiang; Elaine C Meng; Conrad C Huang; Thomas E Ferrin; Patricia C Babbitt
The Structure Superposition Database.
Nucleic acids research 2003;31(1):505-10.
2003: Doug Stryke; Michiko Kawamoto; Conrad C Huang; Susan J Johns; Leslie A King; Courtney A Harper; Elaine C Meng; Roy E Lee; Alice Yee; Larry L'Italien; Pao-Tien Chuang; Stephen G Young; William C Skarnes; Patricia C Babbitt; Thomas E Ferrin
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells.
Nucleic acids research 2003;31(1):278-81.
2002: Maya K Leabman; Conrad C Huang; Michiko Kawamoto; Susan J Johns; Doug Stryke; Thomas E Ferrin; Joseph DeYoung; Travis Taylor; andrew clark; Ira Herskowitz; Kathleen M Giacomini
Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function.
Pharmacogenetics 2002;12(5):395-405.
2000: Conrad C Huang; Walter R P Novak; Patricia C Babbitt; A I Jewett; Thomas E Ferrin; Teri E Klein
Integrated tools for structural and sequence alignment and analysis.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000;():230-41.
1998: Conrad C Huang; Gregory S Couch; Eric F Pettersen; Thomas E Ferrin; A E Howard; Teri E Klein
The object technology framework: an object-oriented interface to molecular data and its application to collagen.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1998;():349-61.